[gmx-users] Pulling along dihedral angle as the reaction coordinate

Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? Thanks and regards Neeru -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Pulling along dihedral angle as the reaction coordinate

I came across one such application name PLUMED plugin for gromacs, for dihedral restraints as the reaction coordinate. If you can suggest any other application for the same, kindly let me know. --Thanks Neeru On 4/15/13 2:27 AM, neeru sharma wrote: Dear gromacs users, I want

[gmx-users] Re: gmx-users Digest, Vol 107, Issue 81

Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma neeru.bioi...@gmail.com wrote: Dear gromacs users, I am simulating a system of Protein-ion-GTP with One Water molecule. I want to restrain this system (along with this water molecule) for minimization

[gmx-users] Restraining water molecule

=flowed On 3/21/13 4:29 AM, neeru sharma wrote: Message: 6 Date: Wed, 20 Mar 2013 09:04:05 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Restraining water molecule To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caduqwc5

[gmx-users] Restraining water molecule

Dear gromacs users, I am simulating a system of Protein-ion-GTP with One Water molecule. I want to restrain this system (along with this water molecule) for minimization and equilibration. Everytime I run this by specifying the .itp files, it gives the error of misplacement as follows: *This

[gmx-users] Re: gmx-users Digest, Vol 106, Issue 62

On 2/12/13 1:12 AM, neeru sharma wrote: Dear Gromacs Users, I have simulated a system of protein-ion complex. As a part of the analysis, I want to see whether there are any H-bonds or other interactions between the active site residues and the water surrounding those residues. I

[gmx-users] Bins in wham analysis

: 1) Should I use more than 15 bins in my case, and the one that gives proper overlap in histogram ? 2) Or any number of bins (even if it is less than 12) can be used, if I get proper overlap in my histogram output? Any suggestion is appreciated. -- Thanks and regards, Neeru Sharma -- gmx-users

[gmx-users] Re: Bins in wham analysis

Thanks Justin for your reply. I did see that the default bins value is 200, but I was not sure what does it signify. It says no of bins used in the analysis. That's why I was confused whether it is equal to no. of umbrella sampling simulations we run and give input to g_wham. Thanks for

[gmx-users] Re: Bins in wham analysis

Thanks Stephan for you suggestion. I will try the analysis with larger value of bins. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Bins-in-wham-analysis-tp4999648p4999709.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users

[gmx-users] Bins in wham analysis

: 1) Should I use more than 15 bins in my case, and the one that gives proper overlap in histogram ? 2) Or any number of bins (even if it is less than 12) can be used, if I get proper overlap in my histogram output? Any suggestion is appreciated. -- Thanks and regards, Neeru Sharma -- gmx-users

[gmx-users] Re: Final state not reached in pulling simulation

Dear Thomas, Thanks for ur reply. I have visualized my trajectory and found no water molecule in between. Moreover, there are no residues in between the Residue and GTP molecule too. I feel I have already applied a large force for the pulling. Still I will consider you suggestion. One query

[gmx-users] Re: Final state not reached in pulling simulation

Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the

[gmx-users] Re: Final state not reached in pulling simulation

Thanks Justin for all your comments and suggestion. I am not using any position restraints as of now. But I will try out more parameters and more options. Thanks again. --Neeru -- View this message in context:

[gmx-users] Final state not reached in pulling simulation

also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- gmx-users mailing listgmx

[gmx-users] Final state not reached in pulling simulation

also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- gmx-users mailing listgmx

[gmx-users] Regarding parameters for pull_groups in mdp file for the pull code

Dear Gromacs Users, I have some queries about the parameters in the .mdp file for the pull code. If I want to pull my ligand, towards specific atom/group of atoms from the protein, how am I supposed to mentioned these in the mdp file?

Re: [gmx-users] Regarding parameters for pull_groups in mdp file for the pull code

Thanks Justin for your early response. I was confused about it, but now it's clear. Thanks --Neeru Dear Gromacs Users, I have some queries about the parameters in the .mdp file for the pull code. If I want to pull my ligand, towards specific atom/group of atoms from the protein, how am I

[gmx-users] Re: Regarding umbrella sampling simulations along H-bonds

Dear Christopher Neale, Let me re-frame my question again. Though I am new to US, but I have a basic idea about performing US. My main query lies for these 2 H-bonds: one between Protein and MG and other one between protein and GTP. I want to know if I can perform umbrella sampling to explain

[gmx-users] Re: Re: Regarding umbrella sampling simulations along H-bonds

to calculate some kind of energy barrier or PMF needed to form these 2 H-bonds along the simulation length? Any suggestion is welcome. Thanks, Neeru Dear Neeru Sharma, I know off hand from years of work with Mg-GTP sites, they are realativly rigid/staritforward. If the bonds arn't present

[gmx-users] Regarding umbrella sampling simulations along H-bonds

Dear Gromacs Users, I am simulating a system containing Protein-Mg-GTP complex. I intend to perform the umbrella sampling on the system to calculate PMF and to perform wham analysis. I have generated a series of conformations for the umbrella sampling. My main consideration is towards the 2

[gmx-users] Regarding Free Energy calculation tutorial

system? For example, I have a Protein-Mg-GTP complex (In initial state A, 2 specific H-bonds are absent and in the final state, these 2 H-bonds are present). So, how can I implement this for the calculation of change in free energy to my system? Thanks and Regards, Neeru Sharma CDAC, Pune

[gmx-users] Re: gmx-users Digest, Vol 98, Issue 44

-8859-1; format=flowed On 6/7/12 8:26 AM, neeru sharma wrote: Dear Justin, Greetings of the day!! I am following your tutorial for the calculation of free energy change in gromacs. It says about the change in state A and state B. I have a query regarding these states. What

[gmx-users] Regarding Free energy (Energy barrier) calculation

that was crossed to reach state 2 (2 H-bonds) from state 1. Can you suggest me some way to find this energy barrier in gromacs ? Thanks in anticipation. -- Regards, Neeru Sharma Project Engineer, Molecular Modelling Team, Bioinformatics Group, Centre for Development of Advanced Computing (CDAC

[gmx-users] Problem in visualizing protein-ion complex trajectory in vmd

Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While

[gmx-users] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs

appreciated. Thanks in advance - Neeru Sharma, Pune (India) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe

[gmx-users] Flooding approach and parameters for protein system

and deltaFO in flooding for a protein system ? As, I am new to gromacs, can you please help me regarding the above mentioned matter and how it can be approached with my system? Any help will be highly appreciated. Regards, Neeru Sharma -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: gmx-users Digest, Vol 96, Issue 146

structures. To my knowledge, none of these is implemented directly within GROMACS, but all could be implemented using GROMACS as a dynamics backend. (NEB On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma neeru.bioi...@gmail.com wrote: Dear Gromacs users, I am simulating a system containing

[gmx-users] PLUMED plugin in gromacs for protein system

Dear gromacs users, I am a gromacs user and need some help regarding the implementation of PLUMED plugin in gromacs. I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs which is a 166 residue protein+mg+GTP/GDP complex. I have already carried out classical MD

[gmx-users] Re: Coupling groups for nvt equilibration

Thanks Justin. I have tried both ways now and considering Protein_MG_GDP and Water_ions groups, it is running without any error but Protein_GDP and MG_Water_ions is failing with an error message. Thanks again... Neeru neeru sharma wrote: Thanks Justin. I tried the simulation

[gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation

this situation? If anyone has simulated any similar system with Protein-ion-ligand complex or have faced similar problem, please share with what to do now to resolve this issue or to simulation such a system? Any help will be highly appreciated. Thanks - Neeru Sharma, Pune (India) -- gmx-users

[gmx-users] Re: Coupling groups for nvt equilibration

Thanks Justin. I tried the simulation with Protein_GDP and Water_ions, considering that Water_and_ions group will include MG. But it didn't work showing an error,saying One atom not present in the coupling group. Shall I try to include MG in Water_ions group via make_ndx ? Neeru neeru

[gmx-users] Coupling groups for nvt equilibration

is on tcoupl = V-rescale tc-grps = Protein_MG_GDP Water_and_ions Is this coupling method correct, to treat Protein and Mg as different quantities? Thanks --- Neeru Sharma Pune (India) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: Re: [gmx-users] Problem with GDP parameters generation

in AMBER03 too? Neeru On 10/12/2011 6:25 AM, neeru sharma wrote: Dear gromacs users, I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving unreliable output, I generated Amber topology and coordinate files for GTP molecule. Then, I converted them

[gmx-users] Problem with GDP parameters generation

itself. OR if anybody has the paramters or topology for GDP, can anyone provide me the same so that I can compare and see where the parameters are differing. Thanks Neeru Sharma Pune (India) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] .top to .itp file conversion

other tool to do so. Thanks Neeru Sharma CDAC, Pune (India) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe